Lyme disease and relapsing fever spirochetes vary significantly in their tick vectors, patterns of pathogenicity in vertebrate hosts, and the disease they cause in humans. With the increasing awareness of relapsing fever, we have focused more on how the relapsing fever spirochetes differ from Lyme disease spirochetes. Our approach was first to determine the total genome sequences of three North American relapsing fever spirochetes, which first included Borrelia hermsii DAH and Borrelia turicatae 91E135. The genomes for these spirochetes have been determined and made public through release of the data in GenBank. We have also just completed another genome sequence for Borrelia hermsii MTW, a highly virulent isolate from Southern California. Our comparative analysis has identified several chromosomal loci that are present in the relapsing fever spirochetes but absent in the Lyme disease spirochetes. Several loci unique to relapsing fever spirochetes have been targets for gene inactivation experiments, including a pathway for purine salvage and an enzyme and transporter for glycerol-3-phosphate. Our hypothesis is that both of these pathways that are unique to the relapsing fever spirochetes may contribute to their ability to achieve high cell densities in the blood, densities that are never seen for the Lyme disease spirochetes. High cell densities in the blood correspond to the acute phase during human infections, and in wild vertebrates are the time of infection when spirochetes are most likely taken up during the blood meal of fast-feeding ticks. Also, with our genome databases we have performed proteomic analyses identifying immunoreactive proteins resolved by two dimensional gel electrophoresis and immunoblots. We hope to identify new antigens that will allow us to perform serological discrimination between infections caused by different species of spirochetes.